The Dynamics and Folding Pathways of Naturally Occurring and Engineered Proteins at Atomic Resolution

Abstract

The protein folding problem, the aim to understand how a protein’s amino acid sequence alone is sufficient to dictate its folded structure in a given environment, has confounded scientists for decades. Comprehensive biophysical and structural analysis of individual proteins can provide insight to the forces driving protein folding in general. The synthesis of years of such experimental and computational research on the Engrailed Homeodomain (EnHD) has produced a detailed description of the states populated along its folding pathway. Here, further examination of the folding pathway using all-atom, explicit solvent molecular dynamics simulations provided an atomic-level description of the interactions responsible for transitioning between these states. Simulations of EnHD near its melting temperature showed that the folding and unfolding pathway are the same and support the use of high temperature unfolding simulations to study the folding pathway in reverse. Multi-molecule unfolding simulations of EnHD gave insight to the effects of intermolecular interactions on folding as well as the types of interactions that drive protein aggregation at high temperature. Further work on an engineered, thermostable variant of EnHD showed that heightened dynamics allowed it to remain stable at high temperature by tolerating the increased thermal fluctuations, whereas EnHD’s more geometrically restrictive packing interactions were perturbed at high temperature, causing it to unfold. To investigate how sequence dictates the folded topology of a protein, a unique system consisting of a pair of proteins engineered to have 88% sequence identity but different folds was studied. In this system, seven differing residues alone hold the key to folding to an all-α or α/β structure, and we identified specific contacts in the denatured state stemming from these residues that committed the proteins to their respective folded structures. Further work on this pair of proteins investigated the denatured state of point mutants that knocked out these putative topology-directing interactions. Finally, a review of research on engineered proteins explored the nonnatural folding pathways created by scientists in the absence of natural selection and the contribution of dynamics to successful designs.